How do I store data per user?

Give each user their own instance of an object. The simplest way is to pass the id yourself:

await state("Users", userId).put({ preferences });

If the id is already a route parameter, map the object to it once and drop the argument everywhere else:

1apiker.init({
2  routes: { "/users/:userId/preferences": handler },
3  objectStateMapping: { Users: "userId" },
4  objects: ["Common", "Users"],
5  exports
6});
7 
8// inside the handler, this now resolves to the :userId instance
9await state("Users").put({ preferences });

For anonymous visitors, map to signedIp instead — a stable, signed hash of the caller's address that is safe to use as a key.

Do not put every user in one instance. Cloudflare serialises requests to a single instance, so a shared one becomes the bottleneck for your whole API.